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. 2008 Oct 1;24(19):2260-2.
doi: 10.1093/bioinformatics/btn411. Epub 2008 Aug 20.

Eigen-R2 for dissecting variation in high-dimensional studies

Lin S Chen  1 , John D Storey
Affiliations

Eigen-R2 for dissecting variation in high-dimensional studies

Lin S Chen et al. Bioinformatics. .

Abstract

We provide a new statistical algorithm and software package called 'eigen-R(2)' for dissecting the variation of a high-dimensional biological dataset with respect to other measured variables of interest. We apply eigen-R(2) to two real-life examples and compare it with simply averaging R(2) over many features.

Availability: An R-package eigenR2 is available at http://www.genomine.org/eigenr2/ and will be made publicly available via Bioconductor.

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Figures

Fig. 1.
Fig. 1.
(a) Tests for linkage among all gene expression trait and marker pairs. A dot indicates significant linkage. (b) Genome-wide comparison of eigen-R2 and mean-R2 values. The dashed horizontal line shows the expected R2 value under no linkage signal. (c) Eigen-R2 and mean-R2 values on Chromosome III, which contains the important MAT locus.
See this image and copyright information in PMC

References

    1. Alter O, et al. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA. 2000;97:10101–10105. - PMC - PubMed
    1. Brem RB, et al. Genetic dissection of transcriptional regulation in budding yeast. Science. 2002;296:752–755. - PubMed
    1. Jin W, et al. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet. 2001;29:389–395. - PubMed
    1. Leek JT, Storey J. Capturing heterogeneity in gene expression studies by “surrogate variable analysis”. PLos Genet. 2007;3:e161. - PMC - PubMed
    1. Morley M, et al. Genetic analysis of genome-wide variation in human gene expression. Nature. 2004;430:743–747. - PMC - PubMed